An Intersection of Math and Medicine: Modeling Cancerous Tumor Kinetics

Anne Talkington with the MAMS function

Anne Talkington with the MAMS function

By Olivia Zhu

Anne Talkington, an undergraduate Mathematics student under the auspices of Richard Durrett, attempts to gain a quantitative grasp on cancer through mathematical modeling. Historically, tumor growth has only been measured in vitro (in a laboratory setting); however, Talkington looks at clinical data from MRIs and mammograms to study how tumors grow in vivo (in the human body).

Talkington is primarily interested in how fast tumors grow and if growth is limited. To analyze these trends, Talkington extracted two time-point measurements of tumor size — one at diagnosis and one immediately before treatment — and compared their change to a variety of mathematical functions. She studied unlimited functions, including the exponential, the power law, and the 2/3 power law, which represents growth limited by surface area, as well as limited functions, including the generalized logistic, which has an upper growth limit, and the Gompertz. Her favorite function is an unlimited function that she created called the Modified Alternating Maclaurin Series, or MAMS, which she originally intended to model microbial growth.

Talkington also examined various types of cancer: breast cancer, liver cancer, tumors of the nerve that connect the ear to the brain, and meningioma, or tumors of the membranes that surround the brain and spinal cord. She expected growth rates among clinical groups to be constant, but she did not generalize between the groups due to demographic bias and other confounding factors.

Ultimately, Talkington found that breast cancer and liver cancer grew exponentially, while tumors of the meninges or vestibulocochlear nerve grew according to the 2/3 power law. Talkington’s work in model-fitting cancer growth will facilitate the administration of effective treatment, which is often growth-stage dependent.

The Mystery Behind the Camel Statue

Knut Schmidt-Nielsen

A file photo of the real Knut Schmidt-Nielsen, not the bronze one, standing with the enigmatic camel statue dedicated to him and his work.

By Olivia Zhu           

The camel statue between the Biology Building and Gross Hall is a staple of Duke’s campus, but the significance behind this landmark is generally unknown.

On Monday, September 22, faculty from the Biology Department gathered for a dedication to remember the man behind the camel statue (or rather, in front of it), Dr. Knut Schmidt-Nielsen, who died in 2007.

Knut Schmidt-Nielsen, who would have turned 99 this Wednesday, was “the father of comparative physiology and integrative biology” and a James B. Duke professor at Duke’s Biology Department starting in 1952.

Schmidt-Nielsen studied the physiology of the camel’s nose, received the International Prize for Biology, and wrote the authoritative text on animal physiology.

Dr. Stephen Wainwright, who was present at the dedication, commissioned the camel to British sculptor Jonathan Kingdon, who finished the bronze camel statue in 1993. The inscription for the statue, “Tell me about yourself, Camel, that I may know myself,” encapsulates Schmidt-Nielsen’s outlook on physiology.

According to Dr. Steven Vogel, who was recruited to Duke’s faculty by Schmidt-Nielsen 49 years ago, Schmidt-Nielsen was actually shy and rather uncomfortable with the statue of himself. Vogel reported that Schmidt-Nielsen greatly advanced the zoology department with his high standards and “great charm and urbanity.”

“You could never say no to Knut,” Vogel said. Schmidt-Nielsen was also reportedly  “a very serious wine drinker”—accordingly, the dedication ceremony ended with wine and champagne.

To learn more about Knut Schmidt-Nielsen, read Vogel’s memoirs or a recommended autobiography, The Camel’s Nose.

Knut Schmidt-Nielsen

The statue as it appears now, with Knut in bronze. (File photo)

Mathematical Restoration of Renaissance Masterpieces

Screen Shot 2014-09-21 at 10.41.22 PM

The Ghissi Masterpiece, missing the ninth panel

By Olivia Zhu

Ninth panel of the Ghissi masterpiece, as reconstructed by Charlotte Caspers

Ninth panel of the Ghissi masterpiece, as reconstructed by Charlotte Caspers

What do Renaissance masterpieces and modern medical images have in common?

The same mathematical technique, “oriented elongated filters,” originally developed to detect blood vessels in medical images can actually be used to detect cracks in digital images of antiquated Renaissance paintings.

On September 19, Henry Yan, Rowena Gan, and Ethan Levine, three undergraduate students at Duke, presented their work on oriented elongated filters and many other techniques to the Math Department. Yan, Gan, and Levine performed summer research to detect and correct cracks in the digitized Ghissi masterpiece, an altarpiece done by 14-century Italian painter Francescuccio di Cecco Ghissi. The altarpiece originally consisted of nine panels, but one was lost in the annals of history and has been recently reconstructed by artist and art historian Charlotte Caspers.

The role of the three undergrads was to digitally rejuvenate the panels of the Ghissi masterpiece, which had faded and accumulated cracks in paint layers because of weathering factors like pressure and temperature. Using various mathematical analysis techniques based in Matlab, including oriented elongated filters, linear combinations of 2-D

Henry Yan's K-SVD analysis to detect cracks in the image at left

Henry Yan’s K-SVD analysis to detect cracks in the image at left

Gaussian kernels (which essentially create directional filters), K-SVD (which updates atoms to better fit an image), and multi-scale top-hat (which extracts small elements and details from an image), the research group created a “crack map,” which they overlaid on the original image.

Then they instructed the computer to fill in the cracks with the colors directly adjacent to the cracks, thereby creating a smoother, crack-free image—this method is called inpainting.

In the future, Yan, Gan, and Levine hope to optimize the procedures they have already developed to accomplish color remapping to digitally age or refurbish images so that they look contemporary to their historical period, and to digitally restore gilding, the presence of gold leaf on paintings.

In the Woods, Stalking Destroying Angels

CAPTION _ WHO IS STUDENT?

Duke student Jordan Forte peers at a Pluteus mushroom growing on a piece of rotten wood.

Story and photos by Robin A. Smith

The dozen or so undergraduate students fanning out in Duke Forest are new to mushroom hunting. The class turns over rotting logs and fallen branches and stirs the leaf litter, on the lookout for signs of fungi. Their guide is Duke professor and mushroom expert Rytas Vilgalys. Like many of the researchers in Duke’s twelve-lab mycology group, he often studies pathogenic fungi known to make people sick, but on this muggy September afternoon Vilgalys is more interested in collecting mushrooms simply for the sake of enjoying them. He plucks a tiny flamingo-pink red chanterelle from the forest floor and gives it a sniff. “They almost smell like apricots,” he said. “You can sprinkle these over your salad.”

CAPTION?

One of the mushrooms the students found was this white coral mushroom growing in leaf litter.

An unusually wet August  makes this a good time for mushrooms and their ilk. Student Jasmine Nee picks up a rotten log studded with what looks like tiny pink bubble gum balls — the fruiting bodies of a slime mold called Lycogala epidendrum. They ooze pinkish goo when popped. “They look like pimples,” she said. Vilgalys has been taking students like Jasmine into the forests of central North Carolina for nearly 30 years as part of his introductory mycology class. Their mission: to collect, photograph and identify one or two new fungi every week. “Think of your photos as the 2014 mushroom calendar for Duke Forest,” he said to the students as they headed down the trail and into the woods. “Don’t let me down.”

CAPTION?

Edible red chanterelles get their color from a natural pigment also found in brightly colored crustaceans and fish.

Today the group is also accompanied by Taylor Lockwood, a world-renowned mushroom photographer whose latest project is a movie about his worldwide quest to find and photograph elusive mushrooms that glow in the dark. Lockwood doesn’t have his tripod or reflectors or other gear with him today. Armed with nothing more than cell phone cameras and collecting baskets, he and the students disappear into the loblolly pines and sweetgum trees in ones and twos, and reappear carrying fistfuls of fungi.

ras_shroom_Lockwood_4617

Mushroom photographer Taylor Lockwood shows off some of the mushrooms found in North Carolina forests.

Lockwood passes around a white specimen with a long stalk and gills. It’s a deadly poisonous mushroom called Amanita, also known as the destroying angel. “You can touch it. Just don’t eat it,” Lockwood said. “Destroying angel is such a great name,” Vilgalys said. “It’s like a bike gang.” They find pale-green Russula mushrooms, white coral mushrooms, red chanterelles, pink slime molds and yellow brain fungus, or witches’ butter. There are also waxcaps, jelly babies, puffballs, hedgehog mushrooms, kidney-shaped soft slipper mushrooms, even a creamy yellow mushroom that appears to have a belly button. “That’s called Gerronema strombodes,” Vilgalys said. “They break down wood.” One student points to something at the base of a pine tree that looks like a dried cow patty. It’s a velvet-top fungus, or Phaeolus schweinitzii – known as a source of natural brown pigments often used for dying wool. “We’ve probably got about 20 or 30 species,” Vilgalys said, looking at their assembled mushrooms laid out on a picnic table. Dressed in a green Lithuania t-shirt, he glances down at his cell phone for an update on the United States versus Lithuania game in the Basketball World Cup when he spots something that looks like a crusty dark brown Q-tip poking up through the leaf litter. It’s a type of mushroom known as earth tongues. “Who wants to see something really cool?” he calls to the group.

Students in bio XXXXX are new to mycology, and hope to find  at least two new fungi every week this term.

Students in bio 540 are new to mycology, and hope to find at least two new fungi every week this term.

Joining the Team: Duncan Dodson

duncandodsonHello world! My name is Duncan Dodson. I am a senior from Tulsa, Oklahoma, pursuing a BS in Environmental Science with a focus on Energy and Sustainability. Though my interests and academic pursuits at Duke have shifted over the course of my undergraduate career (I spent over half of it pursuing a mechanical engineering degree), a constant passion has been conservation of the environment. From age six I was involved in the Boy Scouts of America, received my Eagle Scout Award at sixteen, and have been an avid backpacker for five years. I recently co-directed Duke’s experiential education and backpacking based pre-orientation trip, Project WILD, and have been involved with various outdoor and environmental organizations the past three years.

Two things draw me towards exploring environmental issues: the impetus to think selflessly – environmental justice – and the necessity to approach problems on a larger scale – global climate change. Duke and my selective living group Ubuntu have challenged me to explore how we interact with the world around us in both wonderful and destructive ways.

My other budding passion at Duke is education. Challenging knowledge and ideas by informing and listening is a key part of learning. Transitioning from a more homogeneous community in Oklahoma to the vibrant and varied Triangle Area has framed my education in this respect. This is why I applied to write for the Duke Research Blog. Informing others of energy and sustainability research at Duke excites me; having an open forum where exposure to contrary opinions is expected impassions me.

Hopefully my exploration is as intriguing for readers as it is for me!

Joining the Team: Lyndsey Garcia

Hi! My name is Lyndsey Garcia and I’m proud to call myself a Duke student!

I’m a sophomore in the Pratt School of Engineering and I’m still attempting the infamous biomedical engineering, pre-med route. I was born on the naval base in Whidbey Island, Washington but have spent the last ten years in hot, hot Dallas, TX.

Lyndsey Garcia

Lyndsey Garcia

I love to water ski, snowboard, workout, play sports, sleep, eat carbohydrates, and binge watch Netflix shows. I was a big volleyball player in high school and play for the club volleyball team on campus. I used to play positions that were designated for taller girls, but my teammates quickly outgrew me and was sent to the back row. Yet, I found a way to embrace my short stature and love playing defense. Along with volleyball, I work as a lifeguard at the Duke Aquatic pools and peer tutor in organic chemistry.

Some families like to play board games. Some families like to go on exotic vacations. My family likes to listen to podcasts. I listen to Morning Edition when I ride on the bus and to Planet Money when I lift weights. My love for podcasts has helped expand my love for learning. I have learned about current events in Israel, along with different points of view on health care, and new advancements in cancer research. Having already a passion for math and science and an excitement for learning about the newest developments, it was a natural progression that I would seek to combine these interests to join a research blog. The opportunity to report on all the fascinating developments occurring at leading research institution is one of the greatest things I can imagine!

I love Duke and all it has to offer. While getting a first class education, you can cheer for a top ten basketball team. After doing research in the lab, you can toss of Frisbee with your friends in the gardens. Now I can attend interesting lectures and interview my peers on their intriguing research and develop my love of reporting it to all our readers!

A Quiet but Fundamental Case in the Flame Retardant Debate

By Olivia ZhuClose up of sofa in the living room

The dangers of flame retardants have long been the source of public health debate, thrust into the public eye by legislators, non-profit organizations, and special interest groups.

Often missing, though, is the story of the extensive scientific background necessary to ground these arguments: Heather Stapleton, the Dan and Bunny Gabel Associate Professor of Environmental Ethics and Sustainable Environmental Management, and research scientist Ellen Cooper and their teams  fill this role at the Nicholas School of the Environment.

As a former intern at the Center for Environmental Health, where I advocated against legislation that promotes the use of flame retardant chemicals, I was fascinated to learn the technical side of the conversation from Cooper.

Flame retardants have been present in furniture and other foam-based items largely due to fire safety regulations like California’s TB117, which requires home furniture to resist bursting into flame for a certain amount of time. Historically, manufacturers have met this standard by using flame retardant chemicals that may impact brain development in children or even cause cancer. Consequently, foam producers have added flame retardants to all their foam, even foam meant for products not covered under TB117. Evidently, the resulting flame retardant-laden selection of furniture poses a threat to the health of consumers, who effectively have little choice in protecting themselves against potentially dangerous chemicals.

Nicholas school environmental chemist Heather Stapleton in the lab. (Duke Photography)

Nicholas school environmental chemist Heather Stapleton in the lab. (Duke Photography)

Unsurprisingly, scientifically studying flame retardants requires rigorous chemical analysis. Ellen Cooper, along with the Analytical Chemistry Core, specializes in preparing foam samples and running them through mass spectrometers to identify the flame retardants. The Chemistry Core collaborates with the Stapleton Lab to ensure accurate analysis of often-fragile flame retardants. Both are a part of Duke’s Superfund Research Center.

Cooper’s work has been instrumental in the Stapleton lab’s creation of a foam testing service for consumers. In January, the Stapleton lab started the first foam testing service ever open to the public! Now, consumers can send in up to five samples from their furniture to receive complimentary results which are provided by the Analytical Chemistry Core. On the foam testing website, consumers can also find statistics on common sources of flame retardants and information on how to avoid exposure to flame retardants. Through these efforts, the Stapleton lab is allowing consumers to take back their autonomy.

Additionally, Cooper is working to create a database of all collected samples. Currently, there exists no definite data on which manufacturers’ products contain which flame retardants, or how levels of flame retardants in furniture have changed over time. With enough data points,  Cooper and her team hope to create such heat maps or time analyses, making for a more informed debate, and ultimately a more well-protected public.

Summer Restoration in a Bolivian Winter

By Olivia Zhu2014-06-19 10.45.15

My biggest accomplishment this summer was being able to call the mountains of Bolivia home. Far away from the lecture halls of Duke, I encountered a profound, alternative education that included everything from learning traditional dances to working in a rural hospital laboratory to raising pigs.

Of course, living in Bolivia for two months had its challenges, like a diet in which potatoes were considered vegetables, repeated food poisoning from chicha, the local alcoholic drink consisting of fermented corn, lack of a consistent water source, many near-car accidents, and most of all a deep-seated machismo, but I feel that these were all almost inextricable aspects of a culture that left such a positive impression upon me.

El Hospital Pietro Gamba in Anzaldo, Bolivia

El Hospital Pietro Gamba in Anzaldo served over 69 rural communities in Bolivia

Of course, the inextricability of such factors posed a problem for me as an intern at El Hospital Pietro Gamba encouraging sustainable development to promote public health. Although 80% of children had head lice, a vast majority contracted repeated gastrointestinal bacterial infections, and countless had scabies, the community seemed to get along contentedly. Regardless, with support from the Foundation for Sustainable Development and DukeEngage, my sponsor organizations, I leveraged the relatively new running water system, implemented only 25 years ago, to set in motion a comprehensive lice campaign, to obtain government funding of soap in public restrooms for at least two years, and to create preventative medicine informational materials.

The majority of my education, though, occurred outside the scope of my project. Most importantly, I’ve learned to openly embrace different forms of learning, like relaxation or soccer, that energize me to wholeheartedly pursue my rigorous biophysics career, which I am so fortunate to have at one of the best universities in the world.

The idea of the Aymara New Year illustrates my mentality poignantly: on the first day of the Aymara New Year, traditional Bolivians wish for health, prosperity, and happiness, just as we do in the United States. However, they have a deeper connection with Pachamama, or Mother Nature: on New Year’s Day, they wake up early in the morning to stand on the ground barefoot, awaiting the first rays of the sun. They believe that watching these rays rise above the horizon and light the earth will bring them energy for the entire year. In this, the Aymara New Year represents both personal aspiration and attenuation with the environment.

Similarly, I now aim to maintain a balance between self and surroundings: I hope to be more attuned to the world around me rather than single-mindedly submersing myself in quantum physics, as I believe that varied experiences will infuse me with energy in whatever I pursue. Now, back at Duke for the start of my junior year, I’m excited to begin blogging again and to continue my adventures and education here on campus.

The Aymara sunrise on June 21, 2014.

The Aymara sunrise on June 21, 2014.

Chimpanzee Voices From the Past Go Digital, Open Access

By Karl Leif Bates

A treasure trove of chimpanzee audio recordings from the 1970s has been posted on an open access site for study by a team that includes Evolutionary Anthropology chair Anne Pusey, who also directs Duke’s Jane Goodall Institute Research Center.

An image from the  Scientific Data paper shows the bulky, analog field gear used for making recordings in the 70s.

An image from the Scientific Data paper shows the bulky, analog field gear used for making recordings in the 70s.

Announced this week in the open access journal Scientific Data, the collection includes more than 1,100 recordings made of 17 immature chimpanzees, totaling 10 hours. The recordings were made between 1971 and 1973 by the late Hetty van de Rijt-Plooij and Frans X. Plooij, Dutch researchers working at Goodall’s study site in Gombe National Park, Tanzania.

Though the Plooij collection was catalogued and annotated — notes which Frans then translated from Dutch to English with support from the National Evolutionary Synthesis Center in Durham — the massive collection has never been studied. Preparation of the metadata for the audio recordings was supported by the National Science Foundation (LTREB-1052693).

What the newly digitized recordings represent is the opportunity to study the development of vocalization over a chimpanzee’s lifetime, Pusey explained. Many of the individuals who were recorded as infants and adolescents subsequently turn up in recordings made by Peter Marler in 1967, Charlotte Uhlenbroek in 1991–1993, and Lisa O’Bryan in 2009–2010.

The authors say, “comparing their adult recordings with their infant/juvenile recordings might be an especially effective way of studying vocal development.”

They’re also just kind of fun to listen to. (Browse the entire catalog here.)

Jane Goodall visited Anne Pusey and the archive of Gombe field notes at Duke in 2011. (Duke Photo)

Jane Goodall visited Anne Pusey and the archive of Gombe field notes at Duke in 2011. (Duke Photo)

This work is the latest in a trend of Duke becoming one of the world’s great centers of longitudinal primate studies. Pusey’s work on this audio collection joins the more than 50 years of observational notes and data from Gombe now housed at Duke; Susan Alberts has led the assembly of life history data from nine different primate field studies into a single database. And nearly 50 years of captive lemur data from the Duke Lemur Center was digitized and just posted a few weeks ago. (Pro version on Scientific Data.)

Futurity Research News Site Turns Five

Guest Post by David Jarmul

Futurity.Org, a website that has shared Duke’s research news with millions of readers around the world, is celebrating its fifth anniversary this week.

(Credit: Paul Albertella/Flickr)

(Credit: Paul Albertella/Flickr)

Launched in 2009, Futurity has since recorded 12 million visits and 16 million page views. Among the approximately 10,000 stories it has published are recent Duke offerings on baboon behavior, the treatment of hepatitis C, species extinction and smoking rates among immigrants.

Michael Schoenfeld, Duke’s vice president for public affairs and government relations, helped launch the site, which presents research from 62 leading universities in the United States and other countries in a colorful, non-technical format designed to reach wider audiences.

“When we started Futurity five years ago we hoped to create a new channel to those interested in thoughtful stories about university research,” Schoenfeld said. “That has tfuturity.org logourned into a very successful venture in digital media, and helped create a model collaboration among the top universities in the world.”

Karl Bates, director of research communications for the Office of News and Communications (and editor of this blog), serves as the university’s “bureau chief” for Futurity, working with researchers and communicators across the campus to identify newsworthy stories. He then works with the Futurity editorial team, based at the University of Rochester, to present the stories on Futurity’s website and social media channels on Facebook, Twitter and Google+.

Schoenfeld, who continues to chair Futurity’s governing board, said the site hopes to build on its success and is considering expanding into new arenas to keep pace with the rapidly changing media landscape.